Best Free Sequence Alignment Software For Mac Rating: 9,1/10 4264 reviews
  • MSAProbs is an open-source protein multiplesequence ailgnment algorithm, achieving the stastistically highest alignment accuracy on popular benchmarks: BALIBASE, PREFAB, SABMARK, OXBENCH, compared to ClustalW, MAFFT, MUSCLE, ProbCons and Probalign.

    • MSAProbs-0.9.7.tar.gz
    • Yongchao Liu
    • Freeware (Free)
    • 931 Kb
    • Windows; Linux
  • ZAE is a Zoomable multiplesequenceAlignment ZAE is a Zoomable multiple sequence Alignment Editor.

    • Zoomable Sequence AlignmentEditor
    • zae
    • Freeware (Free)
    • 311 Kb
    • N/A
  • Swift is a DNA sequencealignment program that produces gapped alignment using the Smith-Waterman algorithm. It takes in a query file (FASTA format) and a reference file (FASTA format) as input. It outputs the reference name, read name, gapped ..

    • Swift Sequence AlignmentProgram
    • pvg09
    • Freeware (Free)
    • 467 Kb
    • Linux
  • A tool to compare two Protein Sequences and show similarities with the help of A tool to compare two Protein Sequences and show similarities with the help of dotplot. N eye app for mac free.

    • seqalign.tar.bz2
    • seqalign
    • Freeware (Free)
    • 50 Kb
    • Windows; Mac; Linux
  • Bioinformatics program for analysing two (currently) or more (in the future) protein sequences and compare them using a Smith-Waterman and/or Needleman-Wunsch algorithms. Also set on gathering inherent statistical analysis from the process and displaying. ..

    • Sequence Alignment Program
    • dharyk
    • Freeware (Free)
    • Windows
  • A fast Smith-Waterman algorithm, implemented on CUDA.

    • High performance sequencealignment usin
    • Vahid Noormofidi
    • Freeware (Free)
    • Windows
  • UGENE is a comprehensive genome analysis suite that features multiple sequence alignment and a complex HMM builder and search module. for WindowsAll.

    • ugene_1_9_0_win_x86.exe
    • UniPro
    • Freeware (Free)
    • WindowsAll
  • PFAAT is a Java-based multiplesequencealignment editor and viewer designed for protein family analysis. You can download PFAAT from ..

    • Protein Family AlignmentAnnotation Tool
    • Jeff Carlson, dcaffrey,Enoch Huang, Simon Xi
    • Freeware (Free)
    • Windows
  • A set of programs for multiplesequencealignment and analysis. The programs use an expandable user interface which allows the addition of external analysis functions without any rewriting of code. The system supports several data types, nucleic and. ..

    • Michigan State Univerisity
    • Freeware (Free)
    • 42.8 Mb
    • Mac OS X 10.4 or later
  • aln2dist is a standalone program that uses a multiplesequencealignment to calculate a set of distance matrices and a set of distance restraints (lower and upper bounds). Also require the pdb structure files of homologous proteins to be used as. ..

    For Samsung Print products, enter the M/C or Model Code found on the product label. Examples: “SL-M2020W/XAA”. Examples: LG534UA. Hp scanjet g3110 software mac. For HP products a product number. Use product model name: - Examples: laserjet pro p1102, DeskJet 2130.

    • aln2distrestraint
    • aln2dist
    • Freeware (Free)
    • 385 Kb
    • BSD; Linux
  • ALTER is a web-based tool to transform between multiplesequencealignment formats. ALTER focuses on the specifications of mainstream alignment and analysis programs rather than on the conversion among more or less specific. ..

    • sing
    • Freeware (Free)
    • 51.16 Mb
    • N/A
  • FSA is a probabilistic multiplesequencealignment algorithm which uses a 'distance-based' approach to aligning homologous protein, RNA or DNA FSA is a probabilistic multiple sequence alignment algorithm which uses a 'distance-based' approach to aligning homologous protein, RNA or DNA sequences.

    • fsa-1.15.7.tar.gz
    • fsa
    • Freeware (Free)
    • 9.61 Mb
    • BSD; Mac; Linux
  1. Best Free Sequence Alignment Software For Mac Pro
  2. Free Sequence Alignment Software
  3. Best Free Sequence Alignment Software For Mac Free


The third is necessary because algorithms for both multiple sequence alignment and structural alignment use heuristics which do not always perform perfectly. The fourth is a great example of how interactive graphical tools enable a worker involved in sequence analysis to conveniently execute a variety if different computational tools to explore.

Multiple Sequence Alignment - Protein Sequence Alignment - Alignment You You - Alignment Alignment - Dish Alignment
Best Free Sequence Alignment Software For Mac
Pages : 1 2 3>

This page is a subsection of the list of sequence alignment software.

Multiple alignment visualization tools typically serve four purposes:

  • Aid general understanding of large-scale DNA or protein alignments
  • Visualize alignments for figures and publication
  • Manually edit and curate automatically generated alignments
  • Analysis in depth

The rest of this article is focused on only multiple global alignments of homologous proteins. The first two are a natural consequence of most representations of alignments and their annotation being human-unreadable and best portrayed in the familiar sequence row and alignment column format, of which examples are widespread in the literature. The third is necessary because algorithms for both multiple sequence alignment and structural alignment use heuristics which do not always perform perfectly. The fourth is a great example of how interactive graphical tools enable a worker involved in sequence analysis to conveniently execute a variety if different computational tools to explore an alignment's phylogenetic implications; or, to predict the structure and functional properties of a specific sequence, e.g., comparative modelling.

Alignment viewers, editors[edit]

Best Free Sequence Alignment Software For Mac Pro

NameStructure prediction tools integratedCan align sequencesCan calculate phylogenetic treesOther featuresFormat supportLicenseCan run on BrowserOperating PlatformsLink
AlanNoNoNoAllows sequence alignments to be viewed quickly and directly in a linux terminal without X-forwardingFASTA, ClustalFree, GPL 3NoLinux TerminalOfficial website
Ale (emacs plugin)NoYesNoNoGenBank, EMBL, FASTA, PHYLIPFree, GPLNoGNU EmacsOfficial website
AliView 2019NoMUSCLE integrated; other programs such as MAFFT can be definedExternal programs such as FastTree can be called from withinFast, easy navigation through unlimited mouse wheel zoom in-out feature. Handles unlimited file size alignments. Degenerate primer design.FASTA, FASTQ, PHYLIP, Nexus, MSF, ClustalFree, GPL 3?Cross-platform -Mac OS,



Official website
alvNoNoNoConsole-based (no GUI), yet with colors. Coding DNA is coloured by codon.FASTA, PHYLIP, Nexus, Clustal, StockholmFree, GPL 3NoCross-platformOfficial website, see also alv on GitHub
arbstructure editable, show bond in helix sequence regions, 2D molecule viewerMUSCLE, MAFFT, ClustalW, ProbCons, FastAligner (region-align+auto-reference)arb-parsimony & -NJ, RAxML, PHYML, Phylip, FastTree2, MrBayesEdits huge alignments and trees. Supports NUCs + AA. Displays codons below DNA. Custom column highlighting (e.g. by conservation profiles). Designs, matches and visualizes probes.FASTA, GenBank, EMBL, NewickProprietary, freeware, arb license, open modifiable sourceNoLinux, Mac OS (homebrew)Official website
Base-By-BaseNoMUSCLEUPGMA, NJ, complete and single linkages, WPMGAVisual summary, percent identity tables, some integrated advanced analysis toolsGenbank, FASTA, EMBEL, Clustal, base-by-base filesProprietary, freeware, must register??Official website
BioEditNoClustalWRudimentary, can read PHYLIPPlasmid drawing, ABI chromatograms,Genbank, FASTA, PHYLIP 3.2 and 4, NBRF-PIRProprietary, freewareNoWindows (95/98/NT/2000/XP)Official website
BioNumericsNoYesYes?Genbank, FASTAProprietary, commercial??Official website
bioSyntaxNoNoNoNative syntax highlighting support for Vim, less, gedit and SublimeFASTA, FASTQ, Clustal, SAM, VCF and moreFree, GPL 3NoVim, Less, GEdit, & SublimeOfficial website
BoxShadeNoNoNoSpecifically for multiple alignmentsMSF format as written by PILEUP, READSEQ, or SEQIO (fmtseq); ALN format as written by ClustalWFree, public domainNoMSDOS, VMSOfficial website
CINEMANo, but can read-show 2D structure annotationsClustalWNoDotplot, 6 frame translation, BlastNexus, MSF, Clustal, FASTA, PHYLIP, PIR, PRINTSProprietary, freewareNoCross-platform -Mac OS, Linux, WindowsOfficial website
CLC viewer (free version)Commercial version onlyClustal, MUSCLE, T-Coffee, MAFFT, Kalign, variousUPGMA, NJWorkflows, blast-genbank searchmanyProprietary, freeware. More options available in commercial versions.No?Official website
ClustalX viewerNoClustalWNJAlignment quality analysisNexus, MSF, Clustal, FASTA, PHYLIPProprietary, freeware for academic useNoCommand lineOfficial website
Cylindrical Alignment AppNoNoNo3D, animation, drilldown, legend selectionBLAST XML, proprietary XML, GFF3, ClustalW, INSDSet, user expandable with XSLTFree, CDDL 1. Available for dual licensing.?Cross-platform -Mac OS, Linux, WindowsOfficial website
Cylindrical BLAST ViewerNoNoNo3D, animation, drilldown, legend selectionBLAST XML, proprietary XML, GFF3, ClustalW, INSDSet, user expandable with XSLTFree, GPL??Official website
DECIPHERYesYesUPGMA, NJ, MLPrimer-Probe design, Chimera findingFASTA, FASTQ, GenBankFree, GPLNoMac OS, WindowsOfficial website
Discovery StudioYesAlign123, ClustalW, S-ALIGNUPGMA, NJ, with bootstrap and best treeVisualizer supports 2D and 3D structure and sequence; full version has comprehensive functionality for protein, nucleotides, moreBSML, EMBL, GB, HELM, Clustal, FASTA, GDE, PDB, SEQ, SPT, ..Proprietary, commercial, Viewer is Freeware?Linux, WindowsOfficial website
DnaSP???Can compute several population genetics statistics, reconstruct haplotypes with PHASEFASTA, Nexus, MEGA, PHYLIPProprietary, commercial, freeware for noncomercial use?Cross-platform -Mac OS, Linux, WindowsOfficial website
DNASTAR Lasergene Molecular Biology SuiteYesYesYesAlign DNA, RNA, protein, or DNA + protein sequences via a variety of pairwise and multiple sequence alignment algorithms, generate phylogenetic trees to predict evolutionary relationships, explore sequence tracks to view GC content, gap fraction, sequence logos, translationABI, DNA Multi-Seq, FASTA, GCG Pileup, GenBank, PhredProprietary, commercial, academic licenses available?Mac OS, WindowsOfficial website
emacs - biomode?????Free, GPL??Official website
FLAKNoCan perform fuzzy whole genome alignmentNoVery fast, highly customisable, visualisation is WYSIWYG with filtering and fuzzy optionsFASTAProprietary, commercial, freeware for noncommercial use??Official website
GenedocNo, but can read-show annotationsPairwiseNo, but can read-show annotationsgel simulation, stats, multiple views, simplemanyProprietary, freeware??Official websitetable of features
GeneiousYes - powered by EMBOSS toolsClustal, MUSCLE, MAUVE, profile, translationUPGMA, NJ, PhyML, MrBayes plugin, PAUP* pluginWhole genome assembly, restriction analysis, cloning, primer design, dotplot, much more>40 file formats imported and exportedProprietary, commercial; personal, floating?Cross-platform - Mac, Windows, LinuxOfficial website
Integrated Genome Browser (IGB)NoNoNoSequences and features from files, URLs, and arbitrary DAS and QuickLoad serversBAM, FASTA, PSLFree, CPL?Cross-platform - Mac, Windows, LinuxOfficial website
interactive Tree Of Life (iTOL)NoNo?Phylogenetic tree viewer-annotation tool which can visualise alignments directly on the tree. Various other dataset types can be displayed in addition to alignments.FASTAProprietary, free useYesBrowserOfficial website
IVisTMSANoClustal Omega, ClustalW2, MAFFT, MUSCLE, BioJava are integrated to construct alignmentTree calculation tool calculates phylogenetic tree using BioJava API and lets user draw trees using ArchaeopteryxSoftware is package of 7 interactive visual tools for multiple sequence alignments. Major focus is manipulating large alignments. Includes MSApad, MSA comparator, MSA reconstruction tool, FASTA generator and MSA ID matrix calculatorClustalW, MSF, PHYLIP, PIR, GDE, NexusProprietary, freeware??
JalviewSecondary structure prediction via JNETClustal, MUSCLE, MAFFT, Probcons, TCoffee via web servicesUPGMA, NJSequences and features from arbitrary and publicly registered DAS servers, PFAM, PDB, EMBL, Uniprot Accession retrieval.FASTA, PFAM, MSF, Clustal, BLC, PIR, StockholmFree, GPLAppletCross-platform -Mac OS, Linux,


Official website
JevtraceIntegrated with structure viewer WebMolNoNoA multivalent browser for sequence alignment, phylogeny, and structure. Performs an interactive Evolutionary Trace and other phylogeny inspired analysis.FASTA, MSF, Clustal, PHYLIP, Newick, PDBProprietary, commercial, freeware for academic use?Cross-platform -Mac OS, Linux,


Official websitemanual
JSAVNoNoNoA JavaScript component allowing integrating an alignment viewer into web pagesAn array of JavaScript objectsFree, GPL 2YesBrowserOfficial website
MaestroYesClustalXYesMapping from sequence to 3D structure, structure-sequence editing-modelingClustal, FASTAPDBProprietary, freeware for academic use??Official website
MEGANoNative ClustalWUPGMA, NJ, ME, MP, with bootstrap and confidence testExtended support to phylogenetics analysisFASTA, Clustal, Nexus, MEGA, etc.Proprietary, freeware, must register??Official website
Molecular Operating Environment (MOE)YesYesYesPart of an extensive collection of applications for sequence to structure, including homology modelling; 3D visualisation, etc.Clustal, FASTA, PDB, EMBL, GCG, GCG_MSF, Genbank, PHYLIP, PIR, raw_seqProprietary??Official website
MSAReveal.orgNoNoNoOptional coloring. Touching AA shows 3-letter code and sequence number. Touching consensus shows AA frequencies in that column. Counts and percentages of aromatics, charged, gaps.FASTAFree, Creative Commons Attribution NonCommercial Share-alike??Official website
Multiseq (VMD plugin)No, but can display and align 3D structuresClustalW, MAFFT, Stamp (Structural)Percent identity, Clustal, MAFFT, StructuralScripting via Tcl, mapping from sequence to 3D structureFASTA, PDB, ALN, PHYLIP, NEXUSProprietary, freeware, but VMD is free for noncommercial use only??Official website
MViewNoNoNoStacked alignments from blast and fasta suites, various MSA format conversions, HTML markup, consensus patternsBLAST search, FASTA search, Clustal, HSSP, FASTA, PIR, MSFFree, GPLNoCross-platform - Mac OS, Linux, WindowsOfficial website
PFAATNo, but can display 3D structuresClustalWNJManual annotation, conservation scoresNexus, MSF, Clustal, FASTA, PFAATProprietary, freeware??Official website
Ralee (emacs plugin for RNA al. editing)?RNA structure??StockholmFree, GPL??Official website
S2S RNA editor2D structureRnalignNoBase-base interactions, 2D-3D viewerFASTA, RnaMLProprietary, freeware??Official website
SeaviewNolocal MUSCLE-ClustalWParsimony, distance methods, PhyMLDot-plot, vim-like editing keysNexus, MSF, Clustal, FASTA, PHYLIP, MASEProprietary, freeware??Official website
SeqotronNoMUSCLE, MAFFTUPGMA, NJ, ML (Physher)Manual alignment, tree visualisationNexus, Clustal, FASTA, PHYLIP, MEGA, Stockholm, NBRF/PIR, GDE flatFree, GPL?Mac OS XOfficial websitepublication
SequilabYesYesNoLink alignment results to analysis tools (Primer design, Gel mobility and Maps, Plasmapper, siRNA design Epitope prediction), Save research logs, Create custom toolbarsAccession number, GI number, PDB ID, FASTA, drag-drop from external URL from within the user interfaceProprietary, freeware??Official website
SeqPupNo????Proprietary, freeware??Official website
SequlatorNoPairwise alignmentNoeasy alignment editingMSFProprietary, freeware??Official website
SnipVizNoNoNo (but can display them)Pure Javascript and HTML; suitable to integrate in websitesFASTA, newickFree, Apache 2.0YesBrowsersOfficial website, publication
StrapJnet, NNPREDICT, Coiled coil, 16 different TM-helix15 different methodsNJDot-plot, structure-neighbors, 3D-superposition, Blast-search, Mutation-SNP analysis, Sequence features, BioJava-interfaceMSF, Stockholm, ClustalW, Nexus, FASTA, PDB, Embl, GenBank, hssp, PfamFree, GPL??Official website
TabletNoNoNoHigh-performance graphical viewer for viewing next generation sequence assemblies and alignments.ACE, AFG, MAQ, SOAP2, SAM, BAM, FASTA, FASTQ, GFF3Free, BSD 2-clause??Official website
UGENEYesMUSCLE, Kalign, ClustalW, ClustalO, ClustalX, MAFFT, T-Coffee, Smith–Waterman algorithmYesManyFASTA, FASTQ, GenBank, EMBL, ABIF, SCF, ClustalW, Stockholm, Newick, PDB, MSF, GFFFree, GPL??Official website
VISSA sequence-structure viewerDSSP secondary structureClustalXNoMapping from sequence to 3D structureClustal, FASTAProprietary, freeware??Official website
DNApyNoMUSCLENoEditing of GenBank files, plasmid drawing, ABI chromatograms,FASTA, FASTQ, GenBankFree, GPL 3??Official website
Alignment AnnotatorYesBy sequence or mixed sequence and structureIncludes ArchaeopteryxDAS and user defined annotations. Scriptable. Export to HTML, Word, Jalview.ManyFree, GPLYesiOS, Android, MS-Mobile,


Official website

Free Sequence Alignment Software

Best free sequence alignment software for mac download

See also[edit]

Best Free Sequence Alignment Software For Mac Free

Retrieved from ''